You really need to adjust the tin foil hat, Algol. It's running beyond Alex Jones at this point.
The EP-3 collision was a planned intercept to shadow long range ELINT collecting EP-3 missions which were targeting Hainan and operating in international airspace (not unlike the US intercepts Soviet bombers on long range missions to test the waters). It was pure buffoonery by "wrong way" Wang Wei. The cover story by the Chinese wasn't any better claiming that the heavy aggressively turned into the fighter (losing style points in an unbelievable lie; imagine the shame of a fighter pilot no longer on the planet who now has his government posthumously claiming he was outmaneuvered by a heavy). In any case it was part of a planned military operation which went wrong. Having SOME parallel to the KAL-007 shootdown where the errant 747 aircraft (which was NOT positively identified on radar) through a tragic chain of events may likely have been mistaken for an RC-135 operating out of Shemya (which were also routinely intercepted by the soviets) which was also gathering ELINT information around UHPP. None of these has anything to do with a civil airliner squawking and talking electing to deviate off route to preclude a dangerous situation.
The Iranian shootdown ALSO has no bearing or similarities. The ships were engaged in a current gun battle and were in a hostile combat zone when the Captain of the Vincennes made a bad call to engage what he thought was a hostile aircraft in a combat zone. Several guard calls were made in this case also. As far as I know there's not a war going on over the skies of China at present.
Flying through storms WILL present a very significant safety hazard. The safety risk of leaving an airway while squawking and talking (and relaying intent) is exceedingly low. The choice is clear.